Variant report

Variant	rs11762792
Chromosome Location	chr7:6148772-6148773
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6046967..6050535-chr7:6141219..6149580,10	K562	blood:
2	chr7:6146902..6150449-chr7:6153024..6156434,3	K562	blood:
3	chr7:6143739..6147263-chr7:6147410..6152468,7	K562	blood:
4	chr7:6143803..6145949-chr7:6148611..6151590,2	MCF-7	breast:
5	chr7:6063078..6065231-chr7:6147878..6150172,2	MCF-7	breast:
6	chr7:6146593..6149096-chr7:6152905..6155783,2	K562	blood:
7	chr7:6142931..6146749-chr7:6148381..6152637,7	K562	blood:
8	chr7:6142947..6145756-chr7:6145999..6148954,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106305	Chromatin interaction
ENSG00000106346	Chromatin interaction
ENSG00000122512	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10085518	0.93[JPT][hapmap];0.89[YRI][hapmap]
rs10248850	0.88[JPT][hapmap]
rs10253805	0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10254043	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10257461	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10265503	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10272684	0.89[CHB][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs12536508	0.89[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs12667826	0.96[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2107854	0.88[JPT][hapmap]
rs28727438	0.81[ASN][1000 genomes]
rs3793205	0.81[JPT][hapmap]
rs3793207	0.94[CHB][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap]
rs4035512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4990112	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61443193	0.80[ASN][1000 genomes]
rs61634333	0.89[ASN][1000 genomes]
rs61729726	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6463528	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6463529	0.86[ASN][1000 genomes]
rs6953775	0.89[ASN][1000 genomes]
rs6961833	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6962026	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6973832	0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6979025	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6979838	0.81[ASN][1000 genomes]
rs7456581	0.82[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap]
rs7780867	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7788049	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810368	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs886675	0.96[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9886265	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
2	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
3	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
5	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
7	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
8	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
9	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
10	nsv1034916	chr7:5934780-6158970	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
11	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
12	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
13	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11762792	EIF2AK1	cis	parietal	SCAN
rs11762792	EIF2AK1	cis	cerebellum	SCAN
rs11762792	MMD2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6145600-6148800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:6145600-6152200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:6145600-6155000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:6145600-6186000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:6145600-6186400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:6145800-6152600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:6145800-6152800	Weak transcription	Small Intestine	intestine
8	chr7:6146000-6152000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:6146200-6150800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:6146200-6152000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:6146200-6152600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:6146200-6152800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:6146200-6155000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:6146400-6149000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:6146400-6149800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:6146400-6149800	Weak transcription	Right Atrium	heart
17	chr7:6146400-6150600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:6146400-6150600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:6146400-6150800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:6146400-6150800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:6146400-6150800	Weak transcription	Lung	lung
22	chr7:6146400-6150800	Weak transcription	Ovary	ovary
23	chr7:6146400-6152800	Weak transcription	Aorta	Aorta
24	chr7:6146400-6157600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr7:6146400-6158800	Weak transcription	Esophagus	oesophagus
26	chr7:6146400-6159400	Weak transcription	Gastric	stomach
27	chr7:6146400-6159800	Weak transcription	Pancreas	Pancrea
28	chr7:6146600-6149000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr7:6146600-6149000	Enhancers	HepG2	liver
30	chr7:6146600-6149200	Weak transcription	Fetal Stomach	stomach
31	chr7:6146600-6150600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:6146600-6150600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr7:6146600-6150600	Weak transcription	Primary B cells from cord blood	blood
34	chr7:6146600-6150600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:6146600-6150600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr7:6146600-6150800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:6146600-6150800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:6146600-6150800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:6146600-6150800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr7:6146600-6150800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:6146600-6150800	Weak transcription	Fetal Muscle Leg	muscle
42	chr7:6146600-6150800	Weak transcription	Fetal Thymus	thymus
43	chr7:6146600-6150800	Weak transcription	Left Ventricle	heart
44	chr7:6146600-6150800	Weak transcription	Spleen	Spleen
45	chr7:6146600-6151000	Weak transcription	Placenta	Placenta
46	chr7:6146600-6152800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr7:6146600-6152800	Weak transcription	Right Ventricle	heart
48	chr7:6146600-6154800	Weak transcription	Psoas Muscle	Psoas
49	chr7:6146600-6155000	Weak transcription	Colonic Mucosa	Colon
50	chr7:6146600-6155000	Weak transcription	Colon Smooth Muscle	Colon

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